Bibplography

Bibliography Setup

The bibliography is loaded and the DOIs, ISBNs and ISSNs are extracted.

Introduction

This report assesses the following in regards to the provided bibliography named bibliography:

Remarks: - Group ID is in the json, but not in the csv. The group ID makes it possible to directly jump to the reference in the Zotero Library online.

Data Quality of the Bibliography

Cleanliness of bibliography

One measure of the cleanliness of a Bibliography is assessed by checking the number of references that have a DOI. The following table gives an overview over some numbers regarding the DOIs, ISBNs and ISSNs in the bibliography.

Entries with DOIs, ISBNs or ISSNs

To identify a reference, the most widely used identifier is the DOI. The following table shows the number of references with a DOI and the number of unique DOIs.

To consider duplicate ISBNs or ISSNs as duplicates entries in the library is not waranted as e.g. differenc chapters of a book can be separate entries in the library and therefore lead toi duplicates.

DOIs: 611 (40.6790945%) - 81 duplicates
ISBNss: 115 (7.6564581%) - 119 duplicates
ISBNss: 563 (37.4833555%) - 298 duplicates

The following DOIs are duplicates in the bibliography. This table should be empty.

Show the code

#|
if (sum(duplicated(bibliography$dois)) > 0) {
    data <- data.frame(
        Type = "doi",
        Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', bibliography$dois[duplicated(bibliography$dois)], bibliography$dois[duplicated(bibliography$dois)])
    )
} else {
    data <- data.frame(
        Type = "doi",
        Identifier = NA
    )
}

data |>
    knitr::kable(
        caption = "Duplicate DOIs in the Bibliography",
        escape = FALSE
    )

Duplicate DOIs in the Bibliography
Type	Identifier
doi	10.1146/annurev-environ-042911-093511
doi	10.1126/science.aaa1788
doi	10.1073/pnas.1211466110/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1211466110
doi	10.1016/j.jhydrol.2011.04.023
doi	10.1080/21513732.2011.634436
doi	10.1007/s10531-015-1019-0
doi	10.1073/pnas.0703873104
doi	10.1080/21513732.2011.634436
doi	10.1016/j.jhydrol.2014.01.055
doi	10.1073/pnas.1013100108
doi	10.1016/j.ecolind.2014.05.023
doi	10.1016/j.cosust.2009.07.006
doi	10.1111/j.1365-294X.2012.05461.x
doi	10.1016/S0020-7519(01)00203-X
doi	10.1016/S0140-6736(12)61678-X
doi	10.1111/j.1469-0691.2008.02691.x
doi	10.1175/JCLI-D-12-00302.1
doi	10.1016/j.gloenvcha.2008.02.001
doi	10.1579/0044-7447(2007)36[614:TAAHNO]2.0.CO;2
doi	10.1525/bio.2009.59.11.6
doi	10.1525/bio.2009.59.11.6
doi	10.1016/S0020-7519(98)00056-3
doi	10.1016/j.ecolind.2014.05.023
doi	10.1016/j.crm.2014.08.002
doi	10.1016/j.ecolind.2014.01.025
doi	10.1016/j.jenvman.2014.09.026
doi	10.1016/j.gloenvcha.2014.08.007
doi	10.1146/annurev-environ-042911-093511
doi	10.1038/nature01833
doi	10.1016/j.gloenvcha.2011.08.005
doi	10.1007/s11069-011-0064-6
doi	10.1016/j.cub.2007.11.054
doi	10.1111/fme.12133
doi	10.1111/j.1467-9493.2008.00343.x
doi	10.1353/lde.2012.0019
doi	10.1016/j.envdev.2015.09.007
doi	10.1016/j.ecolecon.2007.09.018
doi	10.1007/s10750-009-9979-2
doi	10.1146/annurev.polisci.2.1.493
doi	10.1016/j.icesjms.2004.12.006
doi	10.1016/j.gloenvcha.2014.03.001
doi	10.1016/j.jenvman.2010.03.023
doi	10.1017/S1355770X12000551
doi	10.1080/14728028.2014.993431
doi	10.1002/pad.259
doi	10.1111/j.1475-4959.2011.00432.x
doi	10.1111/j.1523-1739.2008.00970.x
doi	10.1080/09500690902981269
doi	10.1017/S0376892910000366
doi	10.1016/j.ecolecon.2016.03.018
doi	10.1073/pnas.1302251110
doi	10.1016/j.envsci.2009.04.002
doi	10.1016/j.envhaz.2006.11.001
doi	10.1111/j.1472-4642.2011.00770.x
doi	10.1111/j.1523-1739.2009.01243.x
doi	10.1080/13504500609469666
doi	10.3390/atmos4040383
doi	10.1016/j.icesjms.2004.12.003
doi	10.3389/fevo.2015.00137
doi	10.1016/j.envdev.2015.06.006
doi	10.1016/j.envsci.2014.10.011
doi	10.1007/s10113-013-0533-4
doi	10.1080/02673843.2012.657657
doi	10.1080/03736245.2017.1299639
doi	10.1016/S0016-7185(01)00027-6
doi	10.1146/annurev.energy.30.050504.144511
doi	10.1016/j.ecolecon.2011.11.012
doi	10.3390/su6107142
doi	10.1016/j.ijdrr.2015.01.007
doi	10.1080/21513732.2011.617711
doi	10.1111/j.1468-0491.2008.00402.x
doi	10.1016/j.cosust.2014.11.002
doi	10.1146/annurev.energy.30.050504.144511
doi	10.1016/j.gloenvcha.2014.03.001
doi	8
doi	10.1016/j.gloenvcha.2011.08.002
doi	10.1016/j.cosust.2013.07.002
doi	10.1016/j.cosust.2014.11.002
doi	10.1016/j.cosust.2015.02.006
doi	10.1111/j.1475-2743.2008.00169.x
doi	10.1111/j.1475-2743.2008.00169.x

Show the code

rm(data)

DOIs in Open Alex

To validate the existence and validity of the DOIs, we check if the DOIs are in the OpenAlex database.

Of the 530 unique DOIs in the library, 89 (16.7924528%) are in not in OpenAlex.

Show the code

data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa, metrics$dois_not_in_oa)
) |>
    IPBES.R::table_dt(caption = "dois_not_in_oa")

Of these -423 are not valid. These are:

Show the code

data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)], metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)])
) |>
    knitr::kable(
        caption = "Non Valid DOIs in the Bibliography",
        escape = FALSE
    )

Non Valid DOIs in the Bibliography
Type	Identifier
doi	8209 [pii]
doi	978-92-5-1066904
doi	10.1641/0006-3568(2004)054[0817:DCPOD]2.0.CO;2
doi	10.1579/0044-7447(2007)36[614:TAAHNO]2.0.CO;2
doi	citeulike-article-id:4423649
doi	www.csuchico.edu/biol/Sociobiology/sociobiologyindex.html
doi	Doi 10.1017/S1355770x08004427
doi	10.3390/
doi	8
doi	10.1579/0044-7447(2007)36[387:cldtpm]2.0.co;2
doi	Artn 19
doi	18
doi	10.1029/2001 WR000355; Döll, P., Kaspar, F., Alcamo, J., Computation of global water availability and water use at the scale of large drainage basins (1999) Math. Geol., 4, pp. 115-122; Döll, P., Kaspar, F., Lehner, B., A global hydrological m(TRUNCADO)
doi	10568/73375
doi	doi.org.proxy2.lib.umanitoba.ca/10.1
doi	1092-8987
doi	Project Code C08-0170-0062, 69 pp.
doi	978-92-650-43-77-0

TODO Finally we check, if these dois exist but are not ingested into OpanAlex. This is done using the doi.org resolver This is disabled at the moment.

Show the code

to_check <- bibliography$dois[!(bibliography$dois %in% dois_works)]

dois_valid <- IPBES.R::doi_valid(bibliography$dois)
dois_openalex <- bibliography$dois %in% dois_works
names(dois_openalex) <- bibliography$dois

dois_exist <- IPBES.R::doi_exists(to_check, cache_file = file.path(".", "cache", "doi_exist.rds"))
dois_not_retracted <- IPBES.R::doi_not_retracted(bibliography$dois, cache_file = file.path(".", "cache", "doi_not_retracted.rds"))

sprintf(
    fmt = paste(
        "Number of references: \t\t %d",
        "Number of DOIs: \t\t %d",
        "Number of Duplicate DOIs: \t %d",
        "Number of DOIs in OpenAlex: \t %d ( %f %)",
        "Number of Existing DOIs: \t %d",
        "Number of Retracted DOIs: \t %d",
        "Percentage of Duplicate DOIs: \t %f",
        sep = "\n"
    ),
    nrow(bibliography),
    sum(!is.na(bibliography$dois)),
    length(bibliography$dois) - length(unique((bibliography$dois))),
    sum(dois_openalex), 100 * sum(dois_openalex) / nrow(bibliography),
    sum(dois_exist),
    sum(!dois_not_retracted),
    ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100
) |> cat()

Show the code

oldopts <- options(knitr.kable.NA = "")
data.frame(
    metrics = c(
        "# References",
        "**DOI**",
        "# DOIs",
        "# Duplicate DOIs",
        "# Existing DOIs",
        "# Retracted DOIs",
        "% Duplicate DOIs",
        "**ISBN**",
        "# ISBNs",
        "# Duplicate ISBNs",
        "**ISSN**",
        "# ISSNs",
        "# Duplicate ISSNs"
    ),
    Value = c(
        nrow(bibliography),
        NA,
        sum(!is.na(bibliography$dois)),
        length(bibliography$dois) - length(unique((bibliography$dois))),
        sum(dois_exist),
        sum(!dois_not_retracted),
        ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100,
        NA,
        sum(!is.na(bibliography$isbns)),
        length(bibliography$isbns) - length(unique((bibliography$isbns))),
        NA,
        sum(!is.na(bibliography$issns)),
        length(bibliography$issns) - length(unique((bibliography$issns)))
    )
) |>
    knitr::kable(
        caption = "Cleanliness of the Bibliography",
    )
options(oldopts)

Contentual and Bibliographic analysis

Publication types

Show the code

bibliography$bibliography |>
    dplyr::group_by(
        Item.Type
    ) |>
    dplyr::summarize(
        count = n()
    ) |>
    dplyr::arrange(
        desc(count)
    ) |>
    knitr::kable()

Item.Type	count
journalArticle	1207
book	144
report	112
bookSection	14
conferencePaper	9
thesis	9
manuscript	7

Year of Publication

Show the code

params$figure_pub_year

NULL

Access Status of References

This is checked by using the OpenAlex retrieved works. Therefore it is li=mited to the works that are on OpenAlex. At the moment, only references with a DOI were retrieved from OpenAlex.

Show the code

params$figure_oa_status

NULL

50 Most often cited Journals

Show the code

params$figure_top_journals

NULL

This table contains all Journals as specified in the Zotero database.

Show the code

params$figure_top_journals_data |>
    IPBES.R::table_dt("cited_journals")

TODO Coutries of Institutes of all authors

This plot only contains the countries with more than 10 references.

Show the code

#|
#| fig-height: 10
#| fig-width: 10

params$figure_top_countries

This table contains all countries and the number of authorship.

Show the code

params$figure_top_country_data |>
    IPBES.R::table_dt("top_countries")